Audrey Farbos

Assessing the performance of the Oxford Nanopore Technologies MinION.

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it. The device has a low capital cost, is by far the most portable DNA sequencer available, and can produce data in real-time. It has numerous prospective applications including improving genome sequence assemblies and resolution of repeat-rich regions. Before such a technology is widely adopted, it is important to assess its performance and limitations in respect of throughput and accuracy. In this study we assessed the performance of the MinION by re-sequencing three bacterial genomes, with very different nucleotide compositions ranging from 28.6% to 70.7%; the high G + C strain was underrepresented in the sequencing reads. We estimate the error rate of the MinION (after base calling) to be 38.2%. Mean and median read lengths were 2 kb and 1 kb respectively, while the longest single read was 98 kb. The whole length of a 5 kb rRNA operon was covered by a single read. As the first nanopore-based single molecule sequencer available to researchers, the MinION is an exciting prospect; however, the current error rate limits its ability to compete with existing sequencing technologies, though we do show that MinION sequence reads can enhance contiguity of de novo assembly when used in conjunction with Illumina MiSeq data.

Quality control on the frontier

In the world of high-throughput sequencing there are numerous challenges to effective data quality control. There are no single quality metrics which are appropriate in all conditions. Here we detail the different open source software used at the Exeter Sequencing Service to provide generic quality control information, as well as more specific metrics for genomic and transcriptomic libraries run on Illumina platforms.

Draft Genome Sequences of Three Newly Identified Species in the Genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T

ABSTRACT Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described species in the Cronobacter genus, which is associated with serious infections of neonates. This is the first report of draft genome sequences for these species.

Draft Genome Sequence of the Earliest Cronobacter sakazakii Sequence Type 4 Strain, NCIMB 8272.

ABSTRACT The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with severe cases of neonatal meningitis and persistence in powdered infant formula. For genome sequencing of the earliest deposited culture collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272, originally isolated from milk powder in 1950.

Draft Genome Sequence of “Candidatus Cronobacter colletis” NCTC 14934T, a New Species in the Genus Cronobacter

ABSTRACT Members of the Cronobacter genus are associated with serious infections in neonates. This is the first report of the draft genome sequence for the newly proposed species Cronobacter colletis.

Draft Genome Sequence of a Meningitic Isolate of Cronobacter sakazakii Clonal Complex 4, Strain 8399

ABSTRACT The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine sequence types, is associated with severe cases of neonatal meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4) strains have been sequenced. C. sakazakii strain 8399, isolated from a case of neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain.

Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia

We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide polymorphisms inferred from the sequence data at an average density of approximately one per kilobase of genomic DNA.

TRANSCRIPTIONAL AND EPIGENOMIC PROFILING IN THE ENTORHINAL CORTEX IN AMYLOID AND TAU MOUSE MODELS OF ALZHEIMER’S DISEASE

P1-144 TRANSCRIPTIONAL AND EPIGENOMIC PROFILING IN THE ENTORHINAL CORTEX IN AMYLOID AND TAU MOUSE MODELS OFALZHEIMER’S DISEASE Isabel M. S. Castanho, Tracey K. Murray, Audrey Farbos, Katie Lunnon, David A. Collier, Zeshan Ahmed, Konrad Paszkiewicz, Michael J. O’Neill, Jonathan Mill, University of Exeter, Exeter, United Kingdom; Eli Lilly & Co Ltd, Windlesham, United Kingdom. Contact e-mail: I.Castanho@exeter.ac.uk